The primary objective of this proposal is to develop and deploy cutting edge technologies and chemical genomic tools and to understand the effects of small molecule inhibitors in vivo, and to characterize the model organism Saccharomyces cerevisiae on a systems level. Over the course of the past 3.5 years, as part of an NHGRI-funded project, we have applied three unique genome-wide screens to ~2,000 chemical inhibitors of growth. These data have led to several notable findings, including: 1) novel drug/target interactions, 2) a chemical phenotype for nearly all yeast genes, 3) a systems-level characterization of yeast, and 4) a better understanding of chemical structure-activity relationships as they manifest in vivo. These data have also guided the design of the next-generation chemical genomic assays proposed herein. Using our established bioinformatics and robotics infrastructure, we will design the next generation of assays to interrogate the genome's interaction with small molecules to unprecedented levels of scrutiny, while decreasing cost per chemical. PUBLIC HEALTH RELEVANCE: Small molecules, the central focus of this proposal, make up the majority of FDA approved drugs. Unfortunately, the pharmaceutical industry is currently experiencing sky-rocketing costs (~800 million dollars per new drug) in addition to steadily decreasing productivity. These struggles are attributed in part to unforeseen side-effects of promising drug candidates and by a lack of validated cellular targets to which a drug can bind and elicit a medicinal effect. The specific aims of this proposal address both of these problems.